Multiple sequence alignment - TraesCS3D01G526300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G526300 chr3D 100.000 5569 0 0 1 5569 605067736 605073304 0.000000e+00 10285.0
1 TraesCS3D01G526300 chr3D 91.220 1435 94 12 2822 4230 605160118 605161546 0.000000e+00 1923.0
2 TraesCS3D01G526300 chr3D 92.848 741 42 5 995 1730 605156738 605157472 0.000000e+00 1064.0
3 TraesCS3D01G526300 chr3D 94.636 522 20 6 2127 2645 605159603 605160119 0.000000e+00 802.0
4 TraesCS3D01G526300 chr3D 88.889 315 22 6 1804 2117 605158104 605158406 5.270000e-100 375.0
5 TraesCS3D01G526300 chr3D 97.143 140 4 0 4276 4415 605161567 605161706 2.590000e-58 237.0
6 TraesCS3D01G526300 chr3D 84.733 131 16 3 417 546 53830422 53830549 1.630000e-25 128.0
7 TraesCS3D01G526300 chr3D 95.349 43 2 0 1774 1816 605157483 605157525 1.000000e-07 69.4
8 TraesCS3D01G526300 chr3A 91.659 2230 140 18 2811 5020 736128430 736130633 0.000000e+00 3046.0
9 TraesCS3D01G526300 chr3A 88.925 2140 110 49 1 2118 736124768 736126802 0.000000e+00 2521.0
10 TraesCS3D01G526300 chr3A 94.636 522 22 6 2127 2645 736127920 736128438 0.000000e+00 804.0
11 TraesCS3D01G526300 chr3A 92.889 225 14 2 5153 5376 736130684 736130907 5.380000e-85 326.0
12 TraesCS3D01G526300 chr3A 93.902 164 10 0 2646 2809 687031610 687031447 1.200000e-61 248.0
13 TraesCS3D01G526300 chr3A 83.942 137 18 4 417 551 697029843 697029977 1.630000e-25 128.0
14 TraesCS3D01G526300 chr3A 79.227 207 26 12 5376 5569 736131037 736131239 1.630000e-25 128.0
15 TraesCS3D01G526300 chr3B 86.753 2612 211 57 2811 5376 812821257 812823779 0.000000e+00 2782.0
16 TraesCS3D01G526300 chr3B 92.739 1942 67 28 140 2062 812816011 812817897 0.000000e+00 2737.0
17 TraesCS3D01G526300 chr3B 90.155 386 36 2 2225 2610 812819452 812819835 8.330000e-138 501.0
18 TraesCS3D01G526300 chr3B 91.257 183 14 2 2638 2819 177086353 177086534 1.200000e-61 248.0
19 TraesCS3D01G526300 chr3B 92.771 166 11 1 2645 2810 10304649 10304485 7.210000e-59 239.0
20 TraesCS3D01G526300 chr3B 87.745 204 21 4 414 615 812816454 812816253 9.330000e-58 235.0
21 TraesCS3D01G526300 chr3B 97.080 137 4 0 1 137 812811280 812811416 1.210000e-56 231.0
22 TraesCS3D01G526300 chr3B 92.958 71 5 0 550 620 355437379 355437309 2.740000e-18 104.0
23 TraesCS3D01G526300 chr3B 91.667 48 2 2 461 506 758421839 758421792 1.290000e-06 65.8
24 TraesCS3D01G526300 chr4B 83.333 1374 124 49 741 2043 487768401 487769740 0.000000e+00 1171.0
25 TraesCS3D01G526300 chr4B 85.656 488 32 23 4225 4677 487773594 487774078 3.900000e-131 479.0
26 TraesCS3D01G526300 chr4B 86.374 433 44 9 2203 2622 487771247 487771677 5.080000e-125 459.0
27 TraesCS3D01G526300 chr4B 82.991 535 50 21 3550 4074 487772500 487773003 3.960000e-121 446.0
28 TraesCS3D01G526300 chr4B 91.949 236 17 2 2808 3041 487771705 487771940 4.160000e-86 329.0
29 TraesCS3D01G526300 chr4B 87.129 101 7 4 506 602 564593967 564593869 5.900000e-20 110.0
30 TraesCS3D01G526300 chr4D 83.394 1367 119 47 741 2043 396402220 396403542 0.000000e+00 1168.0
31 TraesCS3D01G526300 chr4D 87.945 506 50 7 2125 2621 396405319 396405822 2.240000e-163 586.0
32 TraesCS3D01G526300 chr4D 89.526 401 23 10 4296 4677 396408037 396408437 1.800000e-134 490.0
33 TraesCS3D01G526300 chr4D 84.156 486 39 17 3567 4043 396406659 396407115 2.380000e-118 436.0
34 TraesCS3D01G526300 chr4D 93.913 230 13 1 2813 3041 396405857 396406086 4.130000e-91 346.0
35 TraesCS3D01G526300 chr4D 83.824 136 16 4 416 551 215174021 215173892 2.110000e-24 124.0
36 TraesCS3D01G526300 chr4D 74.812 266 50 10 3279 3529 366973363 366973100 2.740000e-18 104.0
37 TraesCS3D01G526300 chr4A 83.725 1063 99 37 741 1755 77439530 77440566 0.000000e+00 937.0
38 TraesCS3D01G526300 chr4A 85.066 529 63 8 2125 2638 77442606 77443133 4.940000e-145 525.0
39 TraesCS3D01G526300 chr4A 80.000 670 67 35 3550 4200 77443971 77444592 3.080000e-117 433.0
40 TraesCS3D01G526300 chr4A 87.565 386 26 14 4312 4677 77445295 77445678 1.430000e-115 427.0
41 TraesCS3D01G526300 chr4A 91.667 228 12 3 2813 3033 77443161 77443388 5.420000e-80 309.0
42 TraesCS3D01G526300 chr4A 88.265 196 15 5 1856 2043 77440644 77440839 1.560000e-55 228.0
43 TraesCS3D01G526300 chr4A 88.194 144 10 4 412 551 278325892 278325752 1.240000e-36 165.0
44 TraesCS3D01G526300 chr7A 94.578 166 9 0 2645 2810 628831004 628830839 1.990000e-64 257.0
45 TraesCS3D01G526300 chr7A 76.863 255 39 9 3306 3545 691472139 691472388 5.860000e-25 126.0
46 TraesCS3D01G526300 chr6B 93.939 165 10 0 2646 2810 643078782 643078946 3.330000e-62 250.0
47 TraesCS3D01G526300 chr6B 84.962 133 16 3 417 546 462838077 462838208 1.260000e-26 132.0
48 TraesCS3D01G526300 chr7D 91.279 172 14 1 2646 2816 11122871 11122700 3.350000e-57 233.0
49 TraesCS3D01G526300 chr6D 92.121 165 13 0 2646 2810 37456055 37455891 3.350000e-57 233.0
50 TraesCS3D01G526300 chr6D 85.185 135 16 3 417 549 382866342 382866210 9.730000e-28 135.0
51 TraesCS3D01G526300 chr6D 86.364 110 12 2 506 615 312136360 312136254 3.520000e-22 117.0
52 TraesCS3D01G526300 chr6D 83.529 85 8 4 513 594 413075551 413075470 2.150000e-09 75.0
53 TraesCS3D01G526300 chr2D 91.176 170 14 1 2643 2811 639533691 639533860 4.340000e-56 230.0
54 TraesCS3D01G526300 chr6A 90.698 172 15 1 2646 2817 15552691 15552861 1.560000e-55 228.0
55 TraesCS3D01G526300 chr7B 75.373 402 67 13 3171 3545 678662172 678662568 1.240000e-36 165.0
56 TraesCS3D01G526300 chr7B 85.926 135 14 4 417 551 310555440 310555569 7.520000e-29 139.0
57 TraesCS3D01G526300 chr7B 75.285 263 51 9 3279 3529 711341341 711341601 4.560000e-21 113.0
58 TraesCS3D01G526300 chr2B 88.776 98 6 2 515 612 715814711 715814803 1.270000e-21 115.0
59 TraesCS3D01G526300 chr5B 77.941 204 19 13 416 613 472674721 472674538 2.740000e-18 104.0
60 TraesCS3D01G526300 chr5A 93.939 66 4 0 550 615 377936872 377936937 3.550000e-17 100.0
61 TraesCS3D01G526300 chr5A 100.000 29 0 0 648 676 548762970 548762942 3.000000e-03 54.7
62 TraesCS3D01G526300 chr1A 74.627 268 49 10 3279 3529 548307077 548306812 3.550000e-17 100.0
63 TraesCS3D01G526300 chr1A 83.019 106 13 2 301 402 552203508 552203404 2.140000e-14 91.6
64 TraesCS3D01G526300 chr1D 90.566 53 5 0 3493 3545 298499014 298498962 2.780000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G526300 chr3D 605067736 605073304 5568 False 10285.000000 10285 100.000000 1 5569 1 chr3D.!!$F2 5568
1 TraesCS3D01G526300 chr3D 605156738 605161706 4968 False 745.066667 1923 93.347500 995 4415 6 chr3D.!!$F3 3420
2 TraesCS3D01G526300 chr3A 736124768 736131239 6471 False 1365.000000 3046 89.467200 1 5569 5 chr3A.!!$F2 5568
3 TraesCS3D01G526300 chr3B 812816011 812823779 7768 False 2006.666667 2782 89.882333 140 5376 3 chr3B.!!$F3 5236
4 TraesCS3D01G526300 chr4B 487768401 487774078 5677 False 576.800000 1171 86.060600 741 4677 5 chr4B.!!$F1 3936
5 TraesCS3D01G526300 chr4D 396402220 396408437 6217 False 605.200000 1168 87.786800 741 4677 5 chr4D.!!$F1 3936
6 TraesCS3D01G526300 chr4A 77439530 77445678 6148 False 476.500000 937 86.048000 741 4677 6 chr4A.!!$F1 3936

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
992 1070 1.219124 GACCGCAGCCTCTCAATCA 59.781 57.895 0.0 0.0 0.0 2.57 F
2680 7937 0.036294 CTCCGTTTGACCCCCTCTTC 60.036 60.000 0.0 0.0 0.0 2.87 F
3743 9515 0.034337 TAAACGAGACCTTGCGGCTT 59.966 50.000 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2887 8150 0.392336 AGCAATCTCGAGATGCTCCC 59.608 55.0 30.24 18.25 35.53 4.30 R
4502 11085 0.328258 CCTTGGGGAAGTCCACGAAT 59.672 55.0 0.00 0.00 44.25 3.34 R
5076 11678 0.041535 TGGCTGCATCCCCTTTTGAT 59.958 50.0 3.68 0.00 0.00 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.485394 TGCATTATGTACGCCATGGATT 58.515 40.909 18.40 2.89 34.86 3.01
293 294 7.553760 ACTTTGGATTTATTTTGGAATCATGGC 59.446 33.333 0.00 0.00 34.67 4.40
347 348 6.037098 TGTTGGGATTAAAAACAAGTCAACG 58.963 36.000 0.00 0.00 35.95 4.10
446 491 6.376018 CCTCCGTCCCAAAATTATTGTCTTAA 59.624 38.462 0.00 0.00 0.00 1.85
540 585 8.701908 ATACATCCGTATCTAGACAAACCTAA 57.298 34.615 0.00 0.00 32.66 2.69
541 586 7.040473 ACATCCGTATCTAGACAAACCTAAG 57.960 40.000 0.00 0.00 0.00 2.18
542 587 6.832384 ACATCCGTATCTAGACAAACCTAAGA 59.168 38.462 0.00 0.00 0.00 2.10
543 588 6.690194 TCCGTATCTAGACAAACCTAAGAC 57.310 41.667 0.00 0.00 0.00 3.01
544 589 6.182627 TCCGTATCTAGACAAACCTAAGACA 58.817 40.000 0.00 0.00 0.00 3.41
545 590 6.660521 TCCGTATCTAGACAAACCTAAGACAA 59.339 38.462 0.00 0.00 0.00 3.18
546 591 7.341256 TCCGTATCTAGACAAACCTAAGACAAT 59.659 37.037 0.00 0.00 0.00 2.71
547 592 8.627403 CCGTATCTAGACAAACCTAAGACAATA 58.373 37.037 0.00 0.00 0.00 1.90
606 651 3.049912 GACAAGAATTTTGGCACGGAAC 58.950 45.455 0.00 0.00 0.00 3.62
798 852 3.316573 GAGAGGGGAAGTGGGCACG 62.317 68.421 0.00 0.00 36.20 5.34
821 875 5.562696 CGTTCCTAGCAAGATTTTCTTTGCA 60.563 40.000 11.24 0.00 33.78 4.08
822 876 5.633830 TCCTAGCAAGATTTTCTTTGCAG 57.366 39.130 11.24 6.77 33.78 4.41
893 966 7.118971 CCCTGTTTTATTTTCTCACTCTCTCTG 59.881 40.741 0.00 0.00 0.00 3.35
980 1053 2.559698 TCAAATTCCAAGAGACCGCA 57.440 45.000 0.00 0.00 0.00 5.69
992 1070 1.219124 GACCGCAGCCTCTCAATCA 59.781 57.895 0.00 0.00 0.00 2.57
1005 1083 4.386711 CTCTCAATCAATAGCTCATGGCA 58.613 43.478 8.58 0.00 44.79 4.92
1299 1419 0.917648 CAACACGCGTGAACGAACAC 60.918 55.000 42.94 0.00 43.02 3.32
1708 1829 5.012148 ACTTGTAACTGACCTGCTATTGACT 59.988 40.000 0.00 0.00 0.00 3.41
2048 2818 1.073284 GAAGGCCCTCAAGGTACAACA 59.927 52.381 0.00 0.00 38.26 3.33
2049 2819 1.145571 AGGCCCTCAAGGTACAACAA 58.854 50.000 0.00 0.00 38.26 2.83
2050 2820 1.202891 AGGCCCTCAAGGTACAACAAC 60.203 52.381 0.00 0.00 38.26 3.32
2074 2844 1.290203 ACAACACTCAGCAGTCAACG 58.710 50.000 0.00 0.00 0.00 4.10
2117 3180 2.601666 TCCCTGTCTCTGTGCGCT 60.602 61.111 9.73 0.00 0.00 5.92
2118 3181 2.210013 TCCCTGTCTCTGTGCGCTT 61.210 57.895 9.73 0.00 0.00 4.68
2120 3183 2.031516 CCTGTCTCTGTGCGCTTGG 61.032 63.158 9.73 0.00 0.00 3.61
2121 3184 2.031012 TGTCTCTGTGCGCTTGGG 59.969 61.111 9.73 0.00 0.00 4.12
2124 3187 2.031012 CTCTGTGCGCTTGGGTGA 59.969 61.111 9.73 0.00 0.00 4.02
2125 3188 1.597854 CTCTGTGCGCTTGGGTGAA 60.598 57.895 9.73 0.00 0.00 3.18
2626 7861 6.240894 ACTGGACATAGCAATCTTTCAGAAA 58.759 36.000 0.00 0.00 0.00 2.52
2654 7911 8.504812 AAAAACACATTCAGTAGGCAAATTTT 57.495 26.923 0.00 0.00 0.00 1.82
2655 7912 9.606631 AAAAACACATTCAGTAGGCAAATTTTA 57.393 25.926 0.00 0.00 0.00 1.52
2659 7916 8.367156 ACACATTCAGTAGGCAAATTTTAACAT 58.633 29.630 0.00 0.00 0.00 2.71
2660 7917 8.649841 CACATTCAGTAGGCAAATTTTAACATG 58.350 33.333 0.00 0.00 0.00 3.21
2662 7919 6.588719 TCAGTAGGCAAATTTTAACATGCT 57.411 33.333 0.00 0.00 38.79 3.79
2663 7920 6.620678 TCAGTAGGCAAATTTTAACATGCTC 58.379 36.000 0.00 0.00 38.79 4.26
2664 7921 5.807011 CAGTAGGCAAATTTTAACATGCTCC 59.193 40.000 0.00 0.00 38.79 4.70
2665 7922 3.848726 AGGCAAATTTTAACATGCTCCG 58.151 40.909 0.00 0.00 38.79 4.63
2666 7923 3.258123 AGGCAAATTTTAACATGCTCCGT 59.742 39.130 0.00 0.00 38.79 4.69
2667 7924 3.993736 GGCAAATTTTAACATGCTCCGTT 59.006 39.130 0.00 0.00 38.79 4.44
2668 7925 4.450757 GGCAAATTTTAACATGCTCCGTTT 59.549 37.500 0.00 0.00 38.79 3.60
2669 7926 5.373262 GCAAATTTTAACATGCTCCGTTTG 58.627 37.500 0.00 0.00 35.93 2.93
2670 7927 5.176590 GCAAATTTTAACATGCTCCGTTTGA 59.823 36.000 11.72 0.00 35.93 2.69
2671 7928 6.580476 CAAATTTTAACATGCTCCGTTTGAC 58.420 36.000 0.00 0.00 0.00 3.18
2672 7929 3.907894 TTTAACATGCTCCGTTTGACC 57.092 42.857 0.00 0.00 0.00 4.02
2673 7930 1.816074 TAACATGCTCCGTTTGACCC 58.184 50.000 0.00 0.00 0.00 4.46
2674 7931 0.893727 AACATGCTCCGTTTGACCCC 60.894 55.000 0.00 0.00 0.00 4.95
2675 7932 2.046285 CATGCTCCGTTTGACCCCC 61.046 63.158 0.00 0.00 0.00 5.40
2676 7933 2.231380 ATGCTCCGTTTGACCCCCT 61.231 57.895 0.00 0.00 0.00 4.79
2677 7934 2.046217 GCTCCGTTTGACCCCCTC 60.046 66.667 0.00 0.00 0.00 4.30
2678 7935 2.593956 GCTCCGTTTGACCCCCTCT 61.594 63.158 0.00 0.00 0.00 3.69
2679 7936 2.067197 CTCCGTTTGACCCCCTCTT 58.933 57.895 0.00 0.00 0.00 2.85
2680 7937 0.036294 CTCCGTTTGACCCCCTCTTC 60.036 60.000 0.00 0.00 0.00 2.87
2681 7938 0.473117 TCCGTTTGACCCCCTCTTCT 60.473 55.000 0.00 0.00 0.00 2.85
2682 7939 0.400594 CCGTTTGACCCCCTCTTCTT 59.599 55.000 0.00 0.00 0.00 2.52
2683 7940 1.626825 CCGTTTGACCCCCTCTTCTTA 59.373 52.381 0.00 0.00 0.00 2.10
2684 7941 2.614734 CCGTTTGACCCCCTCTTCTTAC 60.615 54.545 0.00 0.00 0.00 2.34
2685 7942 2.038033 CGTTTGACCCCCTCTTCTTACA 59.962 50.000 0.00 0.00 0.00 2.41
2686 7943 3.307480 CGTTTGACCCCCTCTTCTTACAT 60.307 47.826 0.00 0.00 0.00 2.29
2687 7944 4.010349 GTTTGACCCCCTCTTCTTACATG 58.990 47.826 0.00 0.00 0.00 3.21
2688 7945 2.915869 TGACCCCCTCTTCTTACATGT 58.084 47.619 2.69 2.69 0.00 3.21
2689 7946 2.571653 TGACCCCCTCTTCTTACATGTG 59.428 50.000 9.11 0.00 0.00 3.21
2690 7947 2.838202 GACCCCCTCTTCTTACATGTGA 59.162 50.000 9.11 0.00 0.00 3.58
2691 7948 2.840651 ACCCCCTCTTCTTACATGTGAG 59.159 50.000 11.29 11.29 0.00 3.51
2692 7949 2.171448 CCCCCTCTTCTTACATGTGAGG 59.829 54.545 18.10 18.10 42.72 3.86
2693 7950 2.840651 CCCCTCTTCTTACATGTGAGGT 59.159 50.000 21.48 0.00 41.83 3.85
2694 7951 4.030913 CCCCTCTTCTTACATGTGAGGTA 58.969 47.826 21.48 9.68 41.83 3.08
2695 7952 4.469945 CCCCTCTTCTTACATGTGAGGTAA 59.530 45.833 21.48 9.18 41.83 2.85
2696 7953 5.395768 CCCCTCTTCTTACATGTGAGGTAAG 60.396 48.000 21.48 16.34 45.71 2.34
2705 7962 7.786046 TTACATGTGAGGTAAGAAGGTAAGA 57.214 36.000 9.11 0.00 0.00 2.10
2706 7963 6.287589 ACATGTGAGGTAAGAAGGTAAGAG 57.712 41.667 0.00 0.00 0.00 2.85
2707 7964 5.780793 ACATGTGAGGTAAGAAGGTAAGAGT 59.219 40.000 0.00 0.00 0.00 3.24
2708 7965 6.270231 ACATGTGAGGTAAGAAGGTAAGAGTT 59.730 38.462 0.00 0.00 0.00 3.01
2709 7966 7.453752 ACATGTGAGGTAAGAAGGTAAGAGTTA 59.546 37.037 0.00 0.00 0.00 2.24
2710 7967 7.844493 TGTGAGGTAAGAAGGTAAGAGTTAA 57.156 36.000 0.00 0.00 0.00 2.01
2711 7968 8.431910 TGTGAGGTAAGAAGGTAAGAGTTAAT 57.568 34.615 0.00 0.00 0.00 1.40
2712 7969 8.529476 TGTGAGGTAAGAAGGTAAGAGTTAATC 58.471 37.037 0.00 0.00 0.00 1.75
2713 7970 8.751242 GTGAGGTAAGAAGGTAAGAGTTAATCT 58.249 37.037 0.00 0.00 41.27 2.40
2714 7971 8.750298 TGAGGTAAGAAGGTAAGAGTTAATCTG 58.250 37.037 0.00 0.00 38.67 2.90
2715 7972 8.896722 AGGTAAGAAGGTAAGAGTTAATCTGA 57.103 34.615 0.00 0.00 38.67 3.27
2716 7973 8.751242 AGGTAAGAAGGTAAGAGTTAATCTGAC 58.249 37.037 0.00 0.00 38.57 3.51
2739 7996 8.579006 TGACCATTAATTAATGAGATCAATGGC 58.421 33.333 31.05 18.17 44.40 4.40
2740 7997 8.716674 ACCATTAATTAATGAGATCAATGGCT 57.283 30.769 31.05 8.97 44.40 4.75
2741 7998 8.800332 ACCATTAATTAATGAGATCAATGGCTC 58.200 33.333 31.05 0.00 44.40 4.70
2742 7999 8.799367 CCATTAATTAATGAGATCAATGGCTCA 58.201 33.333 31.05 8.63 44.40 4.26
2743 8000 9.841880 CATTAATTAATGAGATCAATGGCTCAG 57.158 33.333 27.20 0.21 44.40 3.35
2744 8001 9.803507 ATTAATTAATGAGATCAATGGCTCAGA 57.196 29.630 9.93 1.94 43.65 3.27
2745 8002 9.803507 TTAATTAATGAGATCAATGGCTCAGAT 57.196 29.630 11.13 6.61 43.65 2.90
2746 8003 7.925043 ATTAATGAGATCAATGGCTCAGATC 57.075 36.000 11.13 0.00 43.65 2.75
2748 8005 6.683312 AATGAGATCAATGGCTCAGATCTA 57.317 37.500 13.39 6.03 46.15 1.98
2749 8006 6.877668 ATGAGATCAATGGCTCAGATCTAT 57.122 37.500 13.39 7.44 46.15 1.98
2750 8007 6.683312 TGAGATCAATGGCTCAGATCTATT 57.317 37.500 13.39 0.00 46.15 1.73
2751 8008 7.787623 TGAGATCAATGGCTCAGATCTATTA 57.212 36.000 13.39 4.47 46.15 0.98
2752 8009 8.376803 TGAGATCAATGGCTCAGATCTATTAT 57.623 34.615 13.39 0.00 46.15 1.28
2753 8010 9.484806 TGAGATCAATGGCTCAGATCTATTATA 57.515 33.333 13.39 0.00 46.15 0.98
2794 8051 3.722908 AAAAAGGAGGTAAGAGGGAGC 57.277 47.619 0.00 0.00 0.00 4.70
2795 8052 2.344093 AAAGGAGGTAAGAGGGAGCA 57.656 50.000 0.00 0.00 0.00 4.26
2796 8053 2.577772 AAGGAGGTAAGAGGGAGCAT 57.422 50.000 0.00 0.00 0.00 3.79
2797 8054 1.799933 AGGAGGTAAGAGGGAGCATG 58.200 55.000 0.00 0.00 0.00 4.06
2798 8055 1.008938 AGGAGGTAAGAGGGAGCATGT 59.991 52.381 0.00 0.00 0.00 3.21
2799 8056 1.840635 GGAGGTAAGAGGGAGCATGTT 59.159 52.381 0.00 0.00 0.00 2.71
2800 8057 3.039011 GGAGGTAAGAGGGAGCATGTTA 58.961 50.000 0.00 0.00 0.00 2.41
2801 8058 3.454812 GGAGGTAAGAGGGAGCATGTTAA 59.545 47.826 0.00 0.00 0.00 2.01
2802 8059 4.080526 GGAGGTAAGAGGGAGCATGTTAAA 60.081 45.833 0.00 0.00 0.00 1.52
2803 8060 5.497474 GAGGTAAGAGGGAGCATGTTAAAA 58.503 41.667 0.00 0.00 0.00 1.52
2804 8061 5.254115 AGGTAAGAGGGAGCATGTTAAAAC 58.746 41.667 0.00 0.00 0.00 2.43
2805 8062 5.014228 AGGTAAGAGGGAGCATGTTAAAACT 59.986 40.000 0.00 0.00 0.00 2.66
2806 8063 5.123979 GGTAAGAGGGAGCATGTTAAAACTG 59.876 44.000 0.00 0.00 0.00 3.16
2807 8064 3.084786 AGAGGGAGCATGTTAAAACTGC 58.915 45.455 0.00 8.36 35.05 4.40
2808 8065 3.084786 GAGGGAGCATGTTAAAACTGCT 58.915 45.455 15.13 15.13 42.14 4.24
2809 8066 3.084786 AGGGAGCATGTTAAAACTGCTC 58.915 45.455 24.03 24.03 46.90 4.26
2882 8145 0.677731 CACAGTGATCCATGGCCGTT 60.678 55.000 6.96 0.00 0.00 4.44
2887 8150 1.526917 GATCCATGGCCGTTCAGGG 60.527 63.158 6.96 0.00 41.48 4.45
2897 8160 1.144936 CGTTCAGGGGGAGCATCTC 59.855 63.158 0.00 0.00 33.73 2.75
3041 8310 9.565090 AATATCAGTGCAAGATATATGTGTGTT 57.435 29.630 18.21 4.13 37.63 3.32
3053 8773 5.964958 ATATGTGTGTTGCTGCTTACTTT 57.035 34.783 0.00 0.00 0.00 2.66
3063 8783 2.648059 CTGCTTACTTTCCATGGGGAG 58.352 52.381 13.02 12.48 46.01 4.30
3094 8816 3.181493 CCATCTACAGTTTGATGCCAAGC 60.181 47.826 9.52 0.00 38.84 4.01
3107 8829 1.748493 TGCCAAGCCAAATTATCCGAC 59.252 47.619 0.00 0.00 0.00 4.79
3108 8830 2.024414 GCCAAGCCAAATTATCCGACT 58.976 47.619 0.00 0.00 0.00 4.18
3139 8864 0.482446 TGGGGAGCACATTTCCTTGT 59.518 50.000 0.00 0.00 35.01 3.16
3184 8909 0.670546 CCTAGGTGTTGAGTGCGGTG 60.671 60.000 0.00 0.00 0.00 4.94
3209 8934 3.071206 GCTCGAGCACCAGGGAGA 61.071 66.667 31.91 0.00 41.59 3.71
3272 8998 7.961325 TTCAAAGCAATTAAAGAAATCCCAC 57.039 32.000 0.00 0.00 0.00 4.61
3302 9038 3.567670 GCACCAACGTGTGAAAATTTG 57.432 42.857 10.00 0.00 42.39 2.32
3310 9046 6.198216 CCAACGTGTGAAAATTTGGTAGAAAG 59.802 38.462 0.00 0.00 33.39 2.62
3424 9169 7.201835 TCCACGTGCGAAAGTATAATGTTATA 58.798 34.615 10.91 0.00 0.00 0.98
3583 9355 7.095607 GCTACTGTATGGAACTATACAATGTGC 60.096 40.741 11.03 7.64 41.53 4.57
3586 9358 6.054941 TGTATGGAACTATACAATGTGCCAG 58.945 40.000 8.20 0.00 44.35 4.85
3590 9362 4.094887 GGAACTATACAATGTGCCAGTGTG 59.905 45.833 15.48 4.90 42.61 3.82
3619 9391 1.794714 AGCATCTTCCGGTCCTACAT 58.205 50.000 0.00 0.00 0.00 2.29
3631 9403 3.131396 GGTCCTACATATTCCAACTGCG 58.869 50.000 0.00 0.00 0.00 5.18
3663 9435 5.554822 TGTTTGCGAGTTAGTTCAAAAGT 57.445 34.783 0.00 0.00 31.29 2.66
3743 9515 0.034337 TAAACGAGACCTTGCGGCTT 59.966 50.000 0.00 0.00 0.00 4.35
3882 9661 9.482627 CTTCCTATAGATGGAGTTGTTGAATAC 57.517 37.037 0.00 0.00 34.76 1.89
3918 9701 3.181329 ACTGACAGGGTATGACATTCCA 58.819 45.455 12.61 0.00 33.11 3.53
4066 9855 5.008613 TCAGCACAAAATCAACTGGAACTAC 59.991 40.000 0.00 0.00 0.00 2.73
4085 9874 6.260870 ACTACGAATGATACTGCTATCAGG 57.739 41.667 0.00 0.00 41.72 3.86
4101 10035 5.047660 GCTATCAGGTTAAGGATCTCGTGAT 60.048 44.000 0.00 0.00 38.41 3.06
4245 10701 1.247567 GTGGTTGTGGCAATAGCACT 58.752 50.000 19.25 0.00 44.61 4.40
4271 10730 2.099098 CCACCACTTCAACAGGACAAAC 59.901 50.000 0.00 0.00 0.00 2.93
4350 10933 2.045708 GGCAACACATCCGCCATGA 61.046 57.895 0.00 0.00 45.52 3.07
4502 11085 2.340809 CAGGCGTTCGTGTACCCA 59.659 61.111 0.00 0.00 0.00 4.51
4645 11247 4.021456 AGAGAAATGTACACATGTCCGTCA 60.021 41.667 8.60 0.00 40.64 4.35
4729 11331 1.133809 AACTAGCAAGGTGGCCCTCA 61.134 55.000 0.00 0.00 41.56 3.86
4761 11363 3.077359 GGGAATGGTCTTGAAGTCTGTG 58.923 50.000 0.00 0.00 0.00 3.66
4817 11419 8.964420 TGTTGAAAAGATATTTTGGATCGTTC 57.036 30.769 2.13 0.00 0.00 3.95
4878 11480 9.739276 AAAACACCATATTCTAGAATGTTCTCA 57.261 29.630 25.22 6.99 38.70 3.27
4964 11566 8.686334 ACTCAAATTTTGTTCTTGTGTCATAGT 58.314 29.630 8.89 0.00 0.00 2.12
4979 11581 8.250143 TGTGTCATAGTAGATGATAACACCAT 57.750 34.615 0.00 0.00 0.00 3.55
4985 11587 9.987272 CATAGTAGATGATAACACCATCTTTGA 57.013 33.333 10.39 0.00 46.03 2.69
5070 11672 9.907229 AGTAATCTTAATAGAAGGGAAACAAGG 57.093 33.333 0.00 0.00 33.20 3.61
5071 11673 9.901172 GTAATCTTAATAGAAGGGAAACAAGGA 57.099 33.333 0.00 0.00 33.20 3.36
5073 11675 9.467796 AATCTTAATAGAAGGGAAACAAGGAAG 57.532 33.333 0.00 0.00 33.20 3.46
5074 11676 7.402862 TCTTAATAGAAGGGAAACAAGGAAGG 58.597 38.462 0.00 0.00 0.00 3.46
5075 11677 2.294449 AGAAGGGAAACAAGGAAGGC 57.706 50.000 0.00 0.00 0.00 4.35
5076 11678 1.499007 AGAAGGGAAACAAGGAAGGCA 59.501 47.619 0.00 0.00 0.00 4.75
5077 11679 2.110721 AGAAGGGAAACAAGGAAGGCAT 59.889 45.455 0.00 0.00 0.00 4.40
5078 11680 2.222227 AGGGAAACAAGGAAGGCATC 57.778 50.000 0.00 0.00 0.00 3.91
5079 11681 1.428912 AGGGAAACAAGGAAGGCATCA 59.571 47.619 0.00 0.00 0.00 3.07
5080 11682 2.158325 AGGGAAACAAGGAAGGCATCAA 60.158 45.455 0.00 0.00 0.00 2.57
5081 11683 2.632512 GGGAAACAAGGAAGGCATCAAA 59.367 45.455 0.00 0.00 0.00 2.69
5082 11684 3.070878 GGGAAACAAGGAAGGCATCAAAA 59.929 43.478 0.00 0.00 0.00 2.44
5083 11685 4.309933 GGAAACAAGGAAGGCATCAAAAG 58.690 43.478 0.00 0.00 0.00 2.27
5127 11729 4.430007 GTGTCATACCATTAGAGACGCAA 58.570 43.478 0.00 0.00 39.00 4.85
5131 11733 5.753438 GTCATACCATTAGAGACGCAATTGA 59.247 40.000 10.34 0.00 0.00 2.57
5135 11737 5.185454 ACCATTAGAGACGCAATTGAATGA 58.815 37.500 10.34 0.00 0.00 2.57
5140 11742 4.256110 AGAGACGCAATTGAATGATGTCA 58.744 39.130 10.34 0.00 32.73 3.58
5171 11773 4.284829 TCTACACATCTGGCAATCAACA 57.715 40.909 0.00 0.00 0.00 3.33
5179 11781 0.961019 TGGCAATCAACAGTCCTTGC 59.039 50.000 6.26 6.26 42.45 4.01
5185 11787 4.573900 CAATCAACAGTCCTTGCTAGAGT 58.426 43.478 0.00 0.00 0.00 3.24
5206 11808 7.493367 AGAGTTGTCTTACTACATCAATAGCC 58.507 38.462 0.00 0.00 0.00 3.93
5216 11818 4.955811 ACATCAATAGCCGAGGTCAATA 57.044 40.909 0.00 0.00 0.00 1.90
5306 11908 5.633830 AGAACTGCAAAACCATATCACAG 57.366 39.130 0.00 0.00 0.00 3.66
5321 11924 9.466497 ACCATATCACAGAAAAGTGTATTTGAT 57.534 29.630 0.00 0.00 40.37 2.57
5398 12135 7.268586 ACAAACATTGTTGGCTTGTTATGTAA 58.731 30.769 2.13 0.00 42.22 2.41
5420 12157 9.431887 TGTAACTTAATCCTTAGATTGTGTCAC 57.568 33.333 0.00 0.00 42.78 3.67
5436 12173 1.525995 CACGTGGCCTTGTCAACCT 60.526 57.895 7.95 0.00 0.00 3.50
5438 12175 0.395173 ACGTGGCCTTGTCAACCTTT 60.395 50.000 3.32 0.00 0.00 3.11
5440 12177 1.398692 GTGGCCTTGTCAACCTTTCA 58.601 50.000 3.32 0.00 0.00 2.69
5441 12178 1.067060 GTGGCCTTGTCAACCTTTCAC 59.933 52.381 3.32 0.00 0.00 3.18
5442 12179 1.341482 TGGCCTTGTCAACCTTTCACA 60.341 47.619 3.32 0.00 0.00 3.58
5443 12180 1.067060 GGCCTTGTCAACCTTTCACAC 59.933 52.381 0.00 0.00 0.00 3.82
5445 12182 3.211045 GCCTTGTCAACCTTTCACACTA 58.789 45.455 0.00 0.00 0.00 2.74
5447 12184 4.196193 CCTTGTCAACCTTTCACACTACA 58.804 43.478 0.00 0.00 0.00 2.74
5449 12186 5.277974 CCTTGTCAACCTTTCACACTACATG 60.278 44.000 0.00 0.00 0.00 3.21
5450 12187 5.029807 TGTCAACCTTTCACACTACATGA 57.970 39.130 0.00 0.00 0.00 3.07
5451 12188 5.432645 TGTCAACCTTTCACACTACATGAA 58.567 37.500 0.00 0.00 34.27 2.57
5452 12189 5.295787 TGTCAACCTTTCACACTACATGAAC 59.704 40.000 0.00 0.00 35.82 3.18
5454 12191 5.295787 TCAACCTTTCACACTACATGAACAC 59.704 40.000 0.00 0.00 35.82 3.32
5455 12192 4.776349 ACCTTTCACACTACATGAACACA 58.224 39.130 0.00 0.00 35.82 3.72
5456 12193 5.189928 ACCTTTCACACTACATGAACACAA 58.810 37.500 0.00 0.00 35.82 3.33
5458 12195 6.321181 ACCTTTCACACTACATGAACACAATT 59.679 34.615 0.00 0.00 35.82 2.32
5459 12196 7.500892 ACCTTTCACACTACATGAACACAATTA 59.499 33.333 0.00 0.00 35.82 1.40
5460 12197 8.514594 CCTTTCACACTACATGAACACAATTAT 58.485 33.333 0.00 0.00 35.82 1.28
5461 12198 9.546909 CTTTCACACTACATGAACACAATTATC 57.453 33.333 0.00 0.00 35.82 1.75
5462 12199 7.609760 TCACACTACATGAACACAATTATCC 57.390 36.000 0.00 0.00 0.00 2.59
5463 12200 7.164803 TCACACTACATGAACACAATTATCCA 58.835 34.615 0.00 0.00 0.00 3.41
5464 12201 7.334171 TCACACTACATGAACACAATTATCCAG 59.666 37.037 0.00 0.00 0.00 3.86
5465 12202 6.599244 ACACTACATGAACACAATTATCCAGG 59.401 38.462 0.00 0.00 0.00 4.45
5468 12205 8.494433 ACTACATGAACACAATTATCCAGGTAT 58.506 33.333 0.00 0.00 0.00 2.73
5469 12206 9.996554 CTACATGAACACAATTATCCAGGTATA 57.003 33.333 0.00 0.00 0.00 1.47
5470 12207 8.677148 ACATGAACACAATTATCCAGGTATAC 57.323 34.615 0.00 0.00 0.00 1.47
5472 12209 9.342308 CATGAACACAATTATCCAGGTATACTT 57.658 33.333 2.25 0.00 0.00 2.24
5473 12210 9.920946 ATGAACACAATTATCCAGGTATACTTT 57.079 29.630 2.25 0.00 0.00 2.66
5477 12214 8.768397 ACACAATTATCCAGGTATACTTTCAGA 58.232 33.333 2.25 0.00 0.00 3.27
5487 12224 8.352942 CCAGGTATACTTTCAGAAAAATATGGC 58.647 37.037 2.25 0.00 0.00 4.40
5488 12225 9.125026 CAGGTATACTTTCAGAAAAATATGGCT 57.875 33.333 2.25 0.00 0.00 4.75
5507 12253 6.399639 TGGCTAATACTGAATACGATCACA 57.600 37.500 0.00 0.00 0.00 3.58
5524 12270 5.444350 CGATCACATAGTACTCGATCCGTAC 60.444 48.000 0.00 10.48 37.96 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.667262 TGGCGTACATAATGCAAATGAAC 58.333 39.130 16.80 0.00 42.33 3.18
8 9 3.982701 CCATGGCGTACATAATGCAAATG 59.017 43.478 0.00 10.08 42.33 2.32
20 21 2.869233 AATTGCAATCCATGGCGTAC 57.131 45.000 13.38 0.00 0.00 3.67
67 68 3.317993 CCCAATATTTTCATCCCCACGTC 59.682 47.826 0.00 0.00 0.00 4.34
138 139 3.189606 TCATGTCACTTCCCCTACCAAT 58.810 45.455 0.00 0.00 0.00 3.16
204 205 3.941483 CGACCTCCTGCATTAACTCAATT 59.059 43.478 0.00 0.00 0.00 2.32
270 271 6.955364 TGCCATGATTCCAAAATAAATCCAA 58.045 32.000 0.00 0.00 32.11 3.53
272 273 7.935210 AGATTGCCATGATTCCAAAATAAATCC 59.065 33.333 0.00 0.00 32.11 3.01
273 274 8.897872 AGATTGCCATGATTCCAAAATAAATC 57.102 30.769 0.00 0.00 33.42 2.17
274 275 9.689501 AAAGATTGCCATGATTCCAAAATAAAT 57.310 25.926 0.00 0.00 0.00 1.40
275 276 9.517868 AAAAGATTGCCATGATTCCAAAATAAA 57.482 25.926 0.00 0.00 0.00 1.40
276 277 8.948145 CAAAAGATTGCCATGATTCCAAAATAA 58.052 29.630 0.00 0.00 0.00 1.40
277 278 7.553402 CCAAAAGATTGCCATGATTCCAAAATA 59.447 33.333 0.00 0.00 35.10 1.40
278 279 6.376018 CCAAAAGATTGCCATGATTCCAAAAT 59.624 34.615 0.00 0.00 35.10 1.82
279 280 5.706369 CCAAAAGATTGCCATGATTCCAAAA 59.294 36.000 0.00 0.00 35.10 2.44
280 281 5.012871 TCCAAAAGATTGCCATGATTCCAAA 59.987 36.000 0.00 0.00 35.10 3.28
281 282 4.531339 TCCAAAAGATTGCCATGATTCCAA 59.469 37.500 0.00 0.00 35.10 3.53
282 283 4.095211 TCCAAAAGATTGCCATGATTCCA 58.905 39.130 0.00 0.00 35.10 3.53
283 284 4.741321 TCCAAAAGATTGCCATGATTCC 57.259 40.909 0.00 0.00 35.10 3.01
284 285 8.897872 ATAAATCCAAAAGATTGCCATGATTC 57.102 30.769 0.00 0.00 44.75 2.52
285 286 9.689501 AAATAAATCCAAAAGATTGCCATGATT 57.310 25.926 0.00 0.00 44.75 2.57
286 287 9.689501 AAAATAAATCCAAAAGATTGCCATGAT 57.310 25.926 0.00 0.00 44.75 2.45
287 288 8.948145 CAAAATAAATCCAAAAGATTGCCATGA 58.052 29.630 0.00 0.00 44.75 3.07
288 289 8.732531 ACAAAATAAATCCAAAAGATTGCCATG 58.267 29.630 0.00 0.00 44.75 3.66
289 290 8.732531 CACAAAATAAATCCAAAAGATTGCCAT 58.267 29.630 0.00 0.00 44.75 4.40
290 291 7.308469 GCACAAAATAAATCCAAAAGATTGCCA 60.308 33.333 0.00 0.00 44.75 4.92
291 292 7.022979 GCACAAAATAAATCCAAAAGATTGCC 58.977 34.615 0.00 0.00 44.75 4.52
292 293 6.737750 CGCACAAAATAAATCCAAAAGATTGC 59.262 34.615 0.00 0.00 44.75 3.56
293 294 7.235777 CCGCACAAAATAAATCCAAAAGATTG 58.764 34.615 0.00 0.00 44.75 2.67
347 348 1.453928 CCCGCATTCCCTCCTTTCC 60.454 63.158 0.00 0.00 0.00 3.13
519 564 6.832384 TGTCTTAGGTTTGTCTAGATACGGAT 59.168 38.462 0.00 0.00 0.00 4.18
520 565 6.182627 TGTCTTAGGTTTGTCTAGATACGGA 58.817 40.000 0.00 0.00 0.00 4.69
521 566 6.446781 TGTCTTAGGTTTGTCTAGATACGG 57.553 41.667 0.00 0.00 0.00 4.02
682 727 5.595952 AGATCCTCCATTAATCCAGCAAAAC 59.404 40.000 0.00 0.00 0.00 2.43
691 736 6.129179 TCCAAAACCAGATCCTCCATTAATC 58.871 40.000 0.00 0.00 0.00 1.75
798 852 5.772521 TGCAAAGAAAATCTTGCTAGGAAC 58.227 37.500 8.13 0.00 36.71 3.62
821 875 6.006275 AGCTCTACAGATTTCTCTCTCTCT 57.994 41.667 0.00 0.00 0.00 3.10
822 876 6.699575 AAGCTCTACAGATTTCTCTCTCTC 57.300 41.667 0.00 0.00 0.00 3.20
893 966 8.715191 AGACTGAGATAGATGATTGTTTTCAC 57.285 34.615 0.00 0.00 0.00 3.18
980 1053 4.505215 CCATGAGCTATTGATTGAGAGGCT 60.505 45.833 0.00 0.00 0.00 4.58
992 1070 0.816825 CACGGCTGCCATGAGCTATT 60.817 55.000 20.29 0.00 44.23 1.73
1299 1419 3.842923 ATGCGACCTCAGCCCGAG 61.843 66.667 0.00 0.00 41.89 4.63
1842 2573 5.317808 TGTTAATTTGCTACAAGCCTACCA 58.682 37.500 0.00 0.00 41.51 3.25
1843 2574 5.890424 TGTTAATTTGCTACAAGCCTACC 57.110 39.130 0.00 0.00 41.51 3.18
1844 2575 6.751888 CCATTGTTAATTTGCTACAAGCCTAC 59.248 38.462 0.00 0.00 41.51 3.18
1845 2576 6.661377 TCCATTGTTAATTTGCTACAAGCCTA 59.339 34.615 0.00 0.00 41.51 3.93
1846 2577 5.480073 TCCATTGTTAATTTGCTACAAGCCT 59.520 36.000 0.00 0.00 41.51 4.58
1847 2578 5.719173 TCCATTGTTAATTTGCTACAAGCC 58.281 37.500 0.00 0.00 41.51 4.35
1848 2579 6.256321 CCATCCATTGTTAATTTGCTACAAGC 59.744 38.462 0.00 0.00 42.82 4.01
1849 2580 7.546358 TCCATCCATTGTTAATTTGCTACAAG 58.454 34.615 0.00 0.00 35.48 3.16
1999 2738 0.754217 GTCCCGGGGAATTTTAGGGC 60.754 60.000 23.50 0.00 41.76 5.19
2048 2818 2.819608 ACTGCTGAGTGTTGTTGTTGTT 59.180 40.909 0.00 0.00 0.00 2.83
2049 2819 2.420022 GACTGCTGAGTGTTGTTGTTGT 59.580 45.455 0.00 0.00 30.16 3.32
2050 2820 2.419673 TGACTGCTGAGTGTTGTTGTTG 59.580 45.455 0.00 0.00 30.16 3.33
2096 2875 1.375268 GCACAGAGACAGGGACAGC 60.375 63.158 0.00 0.00 0.00 4.40
2117 3180 2.107378 TGCCTTGTCATACTTCACCCAA 59.893 45.455 0.00 0.00 0.00 4.12
2118 3181 1.702401 TGCCTTGTCATACTTCACCCA 59.298 47.619 0.00 0.00 0.00 4.51
2120 3183 1.732259 CGTGCCTTGTCATACTTCACC 59.268 52.381 0.00 0.00 0.00 4.02
2121 3184 2.683968 TCGTGCCTTGTCATACTTCAC 58.316 47.619 0.00 0.00 0.00 3.18
2124 3187 3.895232 AGATCGTGCCTTGTCATACTT 57.105 42.857 0.00 0.00 0.00 2.24
2125 3188 3.195610 TGAAGATCGTGCCTTGTCATACT 59.804 43.478 0.00 0.00 0.00 2.12
2292 6128 0.882927 CTCGGGACTGCACGGAAAAA 60.883 55.000 0.00 0.00 42.43 1.94
2307 6144 4.540153 CCAAGTATGGTGGCTCGG 57.460 61.111 0.00 0.00 42.18 4.63
2592 6436 7.549488 AGATTGCTATGTCCAGTTTAGTACAAC 59.451 37.037 0.00 0.00 0.00 3.32
2597 6441 7.168219 TGAAAGATTGCTATGTCCAGTTTAGT 58.832 34.615 0.00 0.00 0.00 2.24
2634 7891 8.649841 CATGTTAAAATTTGCCTACTGAATGTG 58.350 33.333 0.00 0.00 0.00 3.21
2639 7896 6.350110 GGAGCATGTTAAAATTTGCCTACTGA 60.350 38.462 0.00 0.00 35.71 3.41
2640 7897 5.807011 GGAGCATGTTAAAATTTGCCTACTG 59.193 40.000 0.00 0.00 35.71 2.74
2641 7898 5.393027 CGGAGCATGTTAAAATTTGCCTACT 60.393 40.000 0.00 0.00 35.71 2.57
2642 7899 4.798387 CGGAGCATGTTAAAATTTGCCTAC 59.202 41.667 0.00 0.00 35.71 3.18
2643 7900 4.461081 ACGGAGCATGTTAAAATTTGCCTA 59.539 37.500 0.00 0.00 35.71 3.93
2645 7902 3.584834 ACGGAGCATGTTAAAATTTGCC 58.415 40.909 0.00 0.00 35.71 4.52
2646 7903 5.176590 TCAAACGGAGCATGTTAAAATTTGC 59.823 36.000 0.00 0.00 35.34 3.68
2649 7906 5.227152 GGTCAAACGGAGCATGTTAAAATT 58.773 37.500 0.00 0.00 43.54 1.82
2651 7908 3.004944 GGGTCAAACGGAGCATGTTAAAA 59.995 43.478 0.00 0.00 45.90 1.52
2652 7909 2.554893 GGGTCAAACGGAGCATGTTAAA 59.445 45.455 0.00 0.00 45.90 1.52
2653 7910 2.156098 GGGTCAAACGGAGCATGTTAA 58.844 47.619 0.00 0.00 45.90 2.01
2654 7911 1.612199 GGGGTCAAACGGAGCATGTTA 60.612 52.381 0.00 0.00 45.90 2.41
2655 7912 0.893727 GGGGTCAAACGGAGCATGTT 60.894 55.000 0.00 0.00 45.90 2.71
2659 7916 2.852075 AGGGGGTCAAACGGAGCA 60.852 61.111 0.00 0.00 45.90 4.26
2660 7917 2.046217 GAGGGGGTCAAACGGAGC 60.046 66.667 0.00 0.00 43.35 4.70
2662 7919 0.473117 AGAAGAGGGGGTCAAACGGA 60.473 55.000 0.00 0.00 0.00 4.69
2663 7920 0.400594 AAGAAGAGGGGGTCAAACGG 59.599 55.000 0.00 0.00 0.00 4.44
2664 7921 2.038033 TGTAAGAAGAGGGGGTCAAACG 59.962 50.000 0.00 0.00 0.00 3.60
2665 7922 3.782656 TGTAAGAAGAGGGGGTCAAAC 57.217 47.619 0.00 0.00 0.00 2.93
2666 7923 3.655777 ACATGTAAGAAGAGGGGGTCAAA 59.344 43.478 0.00 0.00 0.00 2.69
2667 7924 3.009033 CACATGTAAGAAGAGGGGGTCAA 59.991 47.826 0.00 0.00 0.00 3.18
2668 7925 2.571653 CACATGTAAGAAGAGGGGGTCA 59.428 50.000 0.00 0.00 0.00 4.02
2669 7926 2.838202 TCACATGTAAGAAGAGGGGGTC 59.162 50.000 0.00 0.00 0.00 4.46
2670 7927 2.840651 CTCACATGTAAGAAGAGGGGGT 59.159 50.000 0.00 0.00 0.00 4.95
2671 7928 2.171448 CCTCACATGTAAGAAGAGGGGG 59.829 54.545 17.52 1.25 41.65 5.40
2672 7929 3.550437 CCTCACATGTAAGAAGAGGGG 57.450 52.381 17.52 1.94 41.65 4.79
2673 7930 5.422331 TCTTACCTCACATGTAAGAAGAGGG 59.578 44.000 25.09 12.94 46.74 4.30
2674 7931 6.531503 TCTTACCTCACATGTAAGAAGAGG 57.468 41.667 21.69 21.69 46.74 3.69
2680 7937 7.837863 TCTTACCTTCTTACCTCACATGTAAG 58.162 38.462 0.00 0.00 44.15 2.34
2681 7938 7.453752 ACTCTTACCTTCTTACCTCACATGTAA 59.546 37.037 0.00 0.00 0.00 2.41
2682 7939 6.952358 ACTCTTACCTTCTTACCTCACATGTA 59.048 38.462 0.00 0.00 0.00 2.29
2683 7940 5.780793 ACTCTTACCTTCTTACCTCACATGT 59.219 40.000 0.00 0.00 0.00 3.21
2684 7941 6.287589 ACTCTTACCTTCTTACCTCACATG 57.712 41.667 0.00 0.00 0.00 3.21
2685 7942 6.936968 AACTCTTACCTTCTTACCTCACAT 57.063 37.500 0.00 0.00 0.00 3.21
2686 7943 7.844493 TTAACTCTTACCTTCTTACCTCACA 57.156 36.000 0.00 0.00 0.00 3.58
2687 7944 8.751242 AGATTAACTCTTACCTTCTTACCTCAC 58.249 37.037 0.00 0.00 0.00 3.51
2688 7945 8.750298 CAGATTAACTCTTACCTTCTTACCTCA 58.250 37.037 0.00 0.00 29.16 3.86
2689 7946 8.968969 TCAGATTAACTCTTACCTTCTTACCTC 58.031 37.037 0.00 0.00 29.16 3.85
2690 7947 8.751242 GTCAGATTAACTCTTACCTTCTTACCT 58.249 37.037 0.00 0.00 29.16 3.08
2691 7948 7.980662 GGTCAGATTAACTCTTACCTTCTTACC 59.019 40.741 9.33 0.00 42.68 2.85
2692 7949 8.529476 TGGTCAGATTAACTCTTACCTTCTTAC 58.471 37.037 14.22 0.00 45.15 2.34
2693 7950 8.660295 TGGTCAGATTAACTCTTACCTTCTTA 57.340 34.615 14.22 0.00 45.15 2.10
2694 7951 7.554959 TGGTCAGATTAACTCTTACCTTCTT 57.445 36.000 14.22 0.00 45.15 2.52
2695 7952 7.741554 ATGGTCAGATTAACTCTTACCTTCT 57.258 36.000 14.22 0.00 45.15 2.85
2696 7953 9.886132 TTAATGGTCAGATTAACTCTTACCTTC 57.114 33.333 14.22 0.00 45.15 3.46
2713 7970 8.579006 GCCATTGATCTCATTAATTAATGGTCA 58.421 33.333 29.22 25.73 45.32 4.02
2714 7971 8.800332 AGCCATTGATCTCATTAATTAATGGTC 58.200 33.333 29.22 24.16 45.32 4.02
2715 7972 8.716674 AGCCATTGATCTCATTAATTAATGGT 57.283 30.769 29.22 19.15 45.32 3.55
2716 7973 8.799367 TGAGCCATTGATCTCATTAATTAATGG 58.201 33.333 29.22 21.78 45.85 3.16
2717 7974 9.841880 CTGAGCCATTGATCTCATTAATTAATG 57.158 33.333 25.89 25.89 43.32 1.90
2718 7975 9.803507 TCTGAGCCATTGATCTCATTAATTAAT 57.196 29.630 4.81 4.81 38.50 1.40
2719 7976 9.803507 ATCTGAGCCATTGATCTCATTAATTAA 57.196 29.630 0.00 0.00 38.50 1.40
2720 7977 9.445878 GATCTGAGCCATTGATCTCATTAATTA 57.554 33.333 8.38 0.00 38.50 1.40
2721 7978 8.164733 AGATCTGAGCCATTGATCTCATTAATT 58.835 33.333 0.00 0.00 41.95 1.40
2722 7979 7.691213 AGATCTGAGCCATTGATCTCATTAAT 58.309 34.615 0.00 0.00 41.95 1.40
2723 7980 7.075851 AGATCTGAGCCATTGATCTCATTAA 57.924 36.000 0.00 0.00 41.95 1.40
2724 7981 6.683312 AGATCTGAGCCATTGATCTCATTA 57.317 37.500 0.00 3.02 41.95 1.90
2725 7982 5.570205 AGATCTGAGCCATTGATCTCATT 57.430 39.130 0.00 2.16 41.95 2.57
2726 7983 6.877668 ATAGATCTGAGCCATTGATCTCAT 57.122 37.500 5.18 0.37 43.80 2.90
2727 7984 6.683312 AATAGATCTGAGCCATTGATCTCA 57.317 37.500 5.18 7.87 43.80 3.27
2774 8031 2.986728 TGCTCCCTCTTACCTCCTTTTT 59.013 45.455 0.00 0.00 0.00 1.94
2775 8032 2.632537 TGCTCCCTCTTACCTCCTTTT 58.367 47.619 0.00 0.00 0.00 2.27
2776 8033 2.344093 TGCTCCCTCTTACCTCCTTT 57.656 50.000 0.00 0.00 0.00 3.11
2777 8034 2.122768 CATGCTCCCTCTTACCTCCTT 58.877 52.381 0.00 0.00 0.00 3.36
2778 8035 1.008938 ACATGCTCCCTCTTACCTCCT 59.991 52.381 0.00 0.00 0.00 3.69
2779 8036 1.501582 ACATGCTCCCTCTTACCTCC 58.498 55.000 0.00 0.00 0.00 4.30
2780 8037 4.755266 TTAACATGCTCCCTCTTACCTC 57.245 45.455 0.00 0.00 0.00 3.85
2781 8038 5.014228 AGTTTTAACATGCTCCCTCTTACCT 59.986 40.000 0.00 0.00 0.00 3.08
2782 8039 5.123979 CAGTTTTAACATGCTCCCTCTTACC 59.876 44.000 0.00 0.00 0.00 2.85
2783 8040 5.392057 GCAGTTTTAACATGCTCCCTCTTAC 60.392 44.000 0.00 0.00 37.00 2.34
2784 8041 4.700213 GCAGTTTTAACATGCTCCCTCTTA 59.300 41.667 0.00 0.00 37.00 2.10
2785 8042 3.507622 GCAGTTTTAACATGCTCCCTCTT 59.492 43.478 0.00 0.00 37.00 2.85
2786 8043 3.084786 GCAGTTTTAACATGCTCCCTCT 58.915 45.455 0.00 0.00 37.00 3.69
2787 8044 3.494045 GCAGTTTTAACATGCTCCCTC 57.506 47.619 0.00 0.00 37.00 4.30
2793 8050 4.808558 TGAATGGAGCAGTTTTAACATGC 58.191 39.130 0.00 8.18 40.29 4.06
2794 8051 6.017400 ACTGAATGGAGCAGTTTTAACATG 57.983 37.500 0.00 0.00 43.67 3.21
2795 8052 7.944729 ATACTGAATGGAGCAGTTTTAACAT 57.055 32.000 0.00 0.00 43.67 2.71
2800 8057 9.060347 CATGTATATACTGAATGGAGCAGTTTT 57.940 33.333 13.89 0.00 43.67 2.43
2801 8058 7.663081 CCATGTATATACTGAATGGAGCAGTTT 59.337 37.037 19.24 0.00 43.67 2.66
2802 8059 7.016563 TCCATGTATATACTGAATGGAGCAGTT 59.983 37.037 21.27 0.00 43.67 3.16
2804 8061 6.939622 TCCATGTATATACTGAATGGAGCAG 58.060 40.000 21.27 0.00 41.39 4.24
2805 8062 6.933514 TCCATGTATATACTGAATGGAGCA 57.066 37.500 21.27 7.49 41.39 4.26
2809 8066 7.623630 TCACCATCCATGTATATACTGAATGG 58.376 38.462 19.56 19.56 39.35 3.16
2882 8145 1.456518 CTCGAGATGCTCCCCCTGA 60.457 63.158 6.58 0.00 0.00 3.86
2887 8150 0.392336 AGCAATCTCGAGATGCTCCC 59.608 55.000 30.24 18.25 35.53 4.30
2897 8160 3.795150 GCTTCTGTCTCCTAGCAATCTCG 60.795 52.174 0.00 0.00 33.88 4.04
3041 8310 1.616725 CCCCATGGAAAGTAAGCAGCA 60.617 52.381 15.22 0.00 0.00 4.41
3053 8773 1.500474 GACAGTGATCTCCCCATGGA 58.500 55.000 15.22 0.00 38.75 3.41
3094 8816 1.414919 TCGGGGAGTCGGATAATTTGG 59.585 52.381 0.00 0.00 0.00 3.28
3166 8891 0.033504 ACACCGCACTCAACACCTAG 59.966 55.000 0.00 0.00 0.00 3.02
3209 8934 6.745450 CGTTTTGACATATTGAAAATAGCGGT 59.255 34.615 0.00 0.00 0.00 5.68
3263 8988 1.135402 GCGGAACACATGTGGGATTTC 60.135 52.381 28.64 21.16 34.19 2.17
3286 9022 6.750039 ACTTTCTACCAAATTTTCACACGTTG 59.250 34.615 0.00 0.00 0.00 4.10
3301 9037 6.537301 CCTACAAATCGCAATACTTTCTACCA 59.463 38.462 0.00 0.00 0.00 3.25
3302 9038 6.511282 GCCTACAAATCGCAATACTTTCTACC 60.511 42.308 0.00 0.00 0.00 3.18
3310 9046 4.569162 TGTACAGCCTACAAATCGCAATAC 59.431 41.667 0.00 0.00 0.00 1.89
3399 9144 3.852286 ACATTATACTTTCGCACGTGGA 58.148 40.909 18.88 10.14 0.00 4.02
3440 9185 9.665719 TTTGTGAACACACAGACATATATACAT 57.334 29.630 7.16 0.00 43.81 2.29
3583 9355 1.612950 TGCTATTTTGGTGCACACTGG 59.387 47.619 20.43 2.80 0.00 4.00
3586 9358 3.855689 AGATGCTATTTTGGTGCACAC 57.144 42.857 20.43 8.79 39.63 3.82
3590 9362 2.223572 CCGGAAGATGCTATTTTGGTGC 60.224 50.000 0.00 0.00 0.00 5.01
3631 9403 2.484889 ACTCGCAAACAAGAGAGTTCC 58.515 47.619 0.00 0.00 44.59 3.62
3663 9435 7.942341 ACATTTGTCACCTTATTTTCTCTACCA 59.058 33.333 0.00 0.00 0.00 3.25
3692 9464 6.925718 GCAAGAAAAGAAGCAATTAAGGACTT 59.074 34.615 0.00 0.00 0.00 3.01
3743 9515 1.525077 GAACCTGACCACGTTGCCA 60.525 57.895 0.00 0.00 0.00 4.92
3882 9661 3.649073 TGTCAGTCCACGTACATTCAAG 58.351 45.455 0.00 0.00 0.00 3.02
3918 9701 1.478105 GGCAGAATTTTCCATCCGCTT 59.522 47.619 0.00 0.00 0.00 4.68
4066 9855 6.587990 CCTTAACCTGATAGCAGTATCATTCG 59.412 42.308 7.31 0.00 43.38 3.34
4085 9874 7.872993 TGGATTGATTATCACGAGATCCTTAAC 59.127 37.037 18.76 0.60 35.67 2.01
4123 10057 7.519008 CGACTGCCAGACATATATTTTCCTTTC 60.519 40.741 0.00 0.00 0.00 2.62
4190 10128 2.065906 TTTGCCGCCGAAGTTTCACC 62.066 55.000 0.00 0.00 0.00 4.02
4245 10701 0.751277 CTGTTGAAGTGGTGGTGGCA 60.751 55.000 0.00 0.00 0.00 4.92
4271 10730 8.867112 AAGCTGAATGCATATATCAAGTTTTG 57.133 30.769 0.00 0.00 45.94 2.44
4347 10930 1.002468 GAAGTTGCTGTTGTGCGTCAT 60.002 47.619 0.00 0.00 35.36 3.06
4350 10933 1.024271 ATGAAGTTGCTGTTGTGCGT 58.976 45.000 0.00 0.00 35.36 5.24
4502 11085 0.328258 CCTTGGGGAAGTCCACGAAT 59.672 55.000 0.00 0.00 44.25 3.34
4729 11331 1.561542 GACCATTCCCCTCACATCTGT 59.438 52.381 0.00 0.00 0.00 3.41
4732 11334 2.239654 TCAAGACCATTCCCCTCACATC 59.760 50.000 0.00 0.00 0.00 3.06
4736 11338 2.305927 GACTTCAAGACCATTCCCCTCA 59.694 50.000 0.00 0.00 0.00 3.86
4739 11341 2.040412 ACAGACTTCAAGACCATTCCCC 59.960 50.000 0.00 0.00 0.00 4.81
5059 11661 1.428912 TGATGCCTTCCTTGTTTCCCT 59.571 47.619 0.00 0.00 0.00 4.20
5064 11666 2.634453 CCCTTTTGATGCCTTCCTTGTT 59.366 45.455 0.00 0.00 0.00 2.83
5065 11667 2.250924 CCCTTTTGATGCCTTCCTTGT 58.749 47.619 0.00 0.00 0.00 3.16
5066 11668 1.551883 CCCCTTTTGATGCCTTCCTTG 59.448 52.381 0.00 0.00 0.00 3.61
5067 11669 1.432807 TCCCCTTTTGATGCCTTCCTT 59.567 47.619 0.00 0.00 0.00 3.36
5068 11670 1.084018 TCCCCTTTTGATGCCTTCCT 58.916 50.000 0.00 0.00 0.00 3.36
5069 11671 1.758862 CATCCCCTTTTGATGCCTTCC 59.241 52.381 0.00 0.00 33.81 3.46
5075 11677 0.462789 GGCTGCATCCCCTTTTGATG 59.537 55.000 0.50 0.00 42.01 3.07
5076 11678 0.041535 TGGCTGCATCCCCTTTTGAT 59.958 50.000 3.68 0.00 0.00 2.57
5077 11679 0.899717 GTGGCTGCATCCCCTTTTGA 60.900 55.000 3.68 0.00 0.00 2.69
5078 11680 1.593265 GTGGCTGCATCCCCTTTTG 59.407 57.895 3.68 0.00 0.00 2.44
5079 11681 1.610379 GGTGGCTGCATCCCCTTTT 60.610 57.895 3.68 0.00 0.00 2.27
5080 11682 2.037847 GGTGGCTGCATCCCCTTT 59.962 61.111 3.68 0.00 0.00 3.11
5081 11683 4.431131 CGGTGGCTGCATCCCCTT 62.431 66.667 3.68 0.00 0.00 3.95
5108 11710 5.912892 TCAATTGCGTCTCTAATGGTATGA 58.087 37.500 0.00 0.00 0.00 2.15
5135 11737 4.724399 TGTGTAGAATTTGGTGGTGACAT 58.276 39.130 0.00 0.00 46.14 3.06
5140 11742 4.335416 CCAGATGTGTAGAATTTGGTGGT 58.665 43.478 0.00 0.00 0.00 4.16
5171 11773 5.081032 AGTAAGACAACTCTAGCAAGGACT 58.919 41.667 0.00 0.00 0.00 3.85
5179 11781 9.672086 GCTATTGATGTAGTAAGACAACTCTAG 57.328 37.037 0.00 0.00 31.83 2.43
5185 11787 6.459670 TCGGCTATTGATGTAGTAAGACAA 57.540 37.500 0.00 0.00 31.83 3.18
5398 12135 6.590292 CACGTGACACAATCTAAGGATTAAGT 59.410 38.462 10.90 0.00 39.87 2.24
5420 12157 0.310854 GAAAGGTTGACAAGGCCACG 59.689 55.000 5.01 0.00 0.00 4.94
5436 12173 8.511321 GGATAATTGTGTTCATGTAGTGTGAAA 58.489 33.333 0.00 0.00 37.34 2.69
5438 12175 7.164803 TGGATAATTGTGTTCATGTAGTGTGA 58.835 34.615 0.00 0.00 0.00 3.58
5440 12177 6.599244 CCTGGATAATTGTGTTCATGTAGTGT 59.401 38.462 0.00 0.00 0.00 3.55
5441 12178 6.599244 ACCTGGATAATTGTGTTCATGTAGTG 59.401 38.462 0.00 0.00 0.00 2.74
5442 12179 6.721318 ACCTGGATAATTGTGTTCATGTAGT 58.279 36.000 0.00 0.00 0.00 2.73
5443 12180 8.908786 ATACCTGGATAATTGTGTTCATGTAG 57.091 34.615 0.00 0.00 0.00 2.74
5445 12182 8.494433 AGTATACCTGGATAATTGTGTTCATGT 58.506 33.333 0.00 0.00 0.00 3.21
5447 12184 9.920946 AAAGTATACCTGGATAATTGTGTTCAT 57.079 29.630 0.00 0.00 0.00 2.57
5449 12186 9.391006 TGAAAGTATACCTGGATAATTGTGTTC 57.609 33.333 0.00 0.00 0.00 3.18
5450 12187 9.396022 CTGAAAGTATACCTGGATAATTGTGTT 57.604 33.333 0.00 0.00 0.00 3.32
5451 12188 8.768397 TCTGAAAGTATACCTGGATAATTGTGT 58.232 33.333 0.00 0.00 33.76 3.72
5452 12189 9.613428 TTCTGAAAGTATACCTGGATAATTGTG 57.387 33.333 0.00 0.00 33.76 3.33
5460 12197 9.627123 CCATATTTTTCTGAAAGTATACCTGGA 57.373 33.333 0.00 0.00 29.65 3.86
5461 12198 8.352942 GCCATATTTTTCTGAAAGTATACCTGG 58.647 37.037 2.75 10.83 29.65 4.45
5462 12199 9.125026 AGCCATATTTTTCTGAAAGTATACCTG 57.875 33.333 2.75 3.20 29.65 4.00
5480 12217 9.587772 GTGATCGTATTCAGTATTAGCCATATT 57.412 33.333 0.00 0.00 0.00 1.28
5490 12227 8.657729 CGAGTACTATGTGATCGTATTCAGTAT 58.342 37.037 0.00 0.00 0.00 2.12
5494 12231 7.148457 GGATCGAGTACTATGTGATCGTATTCA 60.148 40.741 15.20 0.00 37.03 2.57
5495 12232 7.181418 GGATCGAGTACTATGTGATCGTATTC 58.819 42.308 15.20 5.94 37.03 1.75
5496 12233 6.183360 CGGATCGAGTACTATGTGATCGTATT 60.183 42.308 15.20 0.00 37.03 1.89
5500 12246 3.432592 ACGGATCGAGTACTATGTGATCG 59.567 47.826 15.20 13.47 37.03 3.69
5524 12270 7.230712 ACCAATAGTACCTTCCAAAGAAAACAG 59.769 37.037 0.00 0.00 0.00 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.